Ultrafest analysis
Stefano Coretta
10/08/2017
Import data
languages <- read_csv("voicing-effect/stimuli/languages.csv")## Parsed with column specification:
## cols(
## speaker = col_character(),
## language = col_character()
## )words <- read_csv("voicing-effect/stimuli/nonce.csv")## Parsed with column specification:
## cols(
## item = col_integer(),
## word = col_character(),
## ipa = col_character(),
## c1 = col_character(),
## c1phonation = col_character(),
## vowel = col_character(),
## anteropost = col_character(),
## height = col_character(),
## c2 = col_character(),
## c2phonation = col_character(),
## c2place = col_character(),
## language = col_character()
## )columns <- c(
"speaker",
"seconds",
"rec.date",
"prompt",
"label",
"TT.displacement.sm",
"TT.velocity",
"TT.velocity.abs",
"TD.displacement.sm",
"TD.velocity",
"TD.velocity.abs"
)
aaa.files <- list.files(
path = "./voicing-effect/results/ultrasound",
pattern = "*-tongue-cart.tsv",
full.names = TRUE
)
tongues <- read_aaa(
aaa.files,
columns,
na.rm = TRUE
) %>%
mutate(word = word(prompt, 2)) %>%
left_join(y = languages) %>%
left_join(y = words) %>%
mutate_if(is.character, as.factor) %>%
group_by(speaker) %>%
mutate(
X.re = rescale(X),
Y.re = rescale(Y)
) %>%
ungroup() %>%
mutate(
vowel.ord = ordered(vowel, levels = c("a", "o")),
c2place.ord = ordered(c2place, levels = c("coronal", "velar")),
c2phonation.ord = ordered(c2phonation, levels = c("voiceless", "voiced"))
)## Parsed with column specification:
## cols(
## .default = col_double(),
## speaker = col_character(),
## rec.date = col_character(),
## prompt = col_character(),
## label = col_character()
## )## See spec(...) for full column specifications.## Parsed with column specification:
## cols(
## .default = col_double(),
## speaker = col_character(),
## rec.date = col_character(),
## prompt = col_character(),
## label = col_character()
## )## See spec(...) for full column specifications.## Parsed with column specification:
## cols(
## .default = col_double(),
## speaker = col_character(),
## rec.date = col_character(),
## prompt = col_character(),
## label = col_character()
## )## See spec(...) for full column specifications.## Parsed with column specification:
## cols(
## .default = col_double(),
## speaker = col_character(),
## rec.date = col_character(),
## prompt = col_character(),
## label = col_character(),
## X_1 = col_character(),
## Y_1 = col_character()
## )## See spec(...) for full column specifications.## Parsed with column specification:
## cols(
## .default = col_double(),
## speaker = col_character(),
## rec.date = col_character(),
## prompt = col_character(),
## label = col_character()
## )## See spec(...) for full column specifications.## Parsed with column specification:
## cols(
## .default = col_double(),
## speaker = col_character(),
## rec.date = col_character(),
## prompt = col_character(),
## label = col_character()
## )## See spec(...) for full column specifications.## Parsed with column specification:
## cols(
## .default = col_double(),
## speaker = col_character(),
## rec.date = col_character(),
## prompt = col_character(),
## label = col_character()
## )## See spec(...) for full column specifications.## Parsed with column specification:
## cols(
## .default = col_double(),
## speaker = col_character(),
## rec.date = col_character(),
## prompt = col_character(),
## label = col_character()
## )## See spec(...) for full column specifications.## Joining, by = "speaker"## Joining, by = c("word", "language")max <- tongues %>%
filter(label %in% c("max_TT", "max_TD"), vowel != "u") %>%
arrange(rec.date, fan.line) %>%
create_event_start("rec.date")
max_it_12 <- max %>%
filter(speaker %in% c("it01", "it02"))
max_pl_23 <- max %>%
filter(speaker %in% c("pl02", "pl03"))
max_pl_34 <- max %>%
filter(speaker %in% c("pl03", "pl04"))Exploration
max %>%
filter(c2place == "coronal", language == "italian") %>%
plot_tongue(geom = "point", alpha = 0.5) +
aes(colour = c2phonation) +
facet_grid(vowel ~ speaker)
max %>%
filter(c2place == "velar", language == "italian") %>%
plot_tongue(geom = "point", alpha = 0.5) +
aes(colour = c2phonation) +
facet_grid(vowel ~ speaker)
max %>%
filter(c2place == "coronal", language == "polish") %>%
ggplot(aes(X, Y, colour = c2phonation)) +
geom_point(alpha = 0.5) +
facet_grid(speaker ~ vowel) +
coord_fixed(0.7)
max %>%
filter(c2place == "coronal", language == "polish") %>%
ggplot(aes(X.re, Y.re, colour = c2phonation)) +
geom_point(alpha = 0.5) +
facet_grid(speaker ~ vowel) +
coord_fixed(0.7)
max %>%
filter(c2place == "velar", language == "polish") %>%
ggplot(aes(X.re, Y.re, colour = c2phonation)) +
geom_point(alpha = 0.5) +
facet_grid(speaker ~ vowel) +
coord_fixed(0.7)
Testing
Comparing fixed effects models works best with ML, otherwise you can use fREML with AIC, but if there is an AR1 model cannot use AIC.
Polish
pl.m1 <- bam(
Y.re ~
X.re +
s(X.re, bs = "cr") +
s(X.re, by = c2phonation.ord, bs = "cr") +
s(X.re, by = c2place.ord, bs = "cr") +
s(X.re, by = vowel.ord, bs = "cr") +
s(X.re, rec.date, bs = "fs", xt = "cr", m = 1, k = 5) +
s(X.re, speaker, bs = "fs", xt = "cr", m = 1, k = 5),
data = max_pl_23,
method = "fREML"
)## Warning in gam.side(sm, X, tol = .Machine$double.eps^0.5): model has
## repeated 1-d smooths of same variable.rho <- start_value_rho(pl.m1)
pl.m1.ar <- bam(
Y.re ~
X.re +
s(X.re, bs = "cr") +
s(X.re, by = c2phonation.ord, bs = "cr") +
s(X.re, by = c2place.ord, bs = "cr") +
s(X.re, by = vowel.ord, bs = "cr") +
s(X.re, rec.date, bs = "fs", xt = "cr", m = 1, k = 5) +
s(X.re, speaker, bs = "fs", xt = "cr", m = 1, k = 5),
data = max_pl_23,
method = "fREML",
rho = rho,
AR.start = max_pl_23$start.event
)## Warning in gam.side(sm, X, tol = .Machine$double.eps^0.5): model has
## repeated 1-d smooths of same variable.summary(pl.m1)##
## Family: gaussian
## Link function: identity
##
## Formula:
## Y.re ~ X.re + s(X.re, bs = "cr") + s(X.re, by = c2phonation.ord,
## bs = "cr") + s(X.re, by = c2place.ord, bs = "cr") + s(X.re,
## by = vowel.ord, bs = "cr") + s(X.re, rec.date, bs = "fs",
## xt = "cr", m = 1, k = 5) + s(X.re, speaker, bs = "fs", xt = "cr",
## m = 1, k = 5)
##
## Parametric coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 0.2474 0.1778 1.392 0.1641
## X.re 0.6437 0.3900 1.651 0.0989 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Approximate significance of smooth terms:
## edf Ref.df F p-value
## s(X.re) 6.804 7.090 32.225 < 2e-16 ***
## s(X.re):c2phonation.ordvoiced 7.958 8.606 7.478 1.56e-08 ***
## s(X.re):c2place.ordvelar 8.825 8.965 85.509 < 2e-16 ***
## s(X.re):vowel.ordo 8.717 8.935 19.070 < 2e-16 ***
## s(X.re,rec.date) 481.302 540.000 19.552 < 2e-16 ***
## s(X.re,speaker) 5.570 8.000 32.388 < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Rank: 592/593
## R-sq.(adj) = 0.958 Deviance explained = 96.3%
## fREML = -6475.4 Scale est. = 0.0015912 n = 4212pl.m1.null <- bam(
Y.re ~
X.re +
s(X.re, bs = "cr") +
s(X.re, by = c2place.ord, bs = "cr") +
s(X.re, by = vowel.ord, bs = "cr") +
s(X.re, rec.date, bs = "fs", xt = "cr", m = 1, k = 5) +
s(X.re, speaker, bs = "fs", xt = "cr", m = 1, k = 5),
data = max_pl_23,
method = "fREML"
)## Warning in gam.side(sm, X, tol = .Machine$double.eps^0.5): model has
## repeated 1-d smooths of same variable.compareML(pl.m1, pl.m1.null)## pl.m1: Y.re ~ X.re + s(X.re, bs = "cr") + s(X.re, by = c2phonation.ord,
## bs = "cr") + s(X.re, by = c2place.ord, bs = "cr") + s(X.re,
## by = vowel.ord, bs = "cr") + s(X.re, rec.date, bs = "fs",
## xt = "cr", m = 1, k = 5) + s(X.re, speaker, bs = "fs", xt = "cr",
## m = 1, k = 5)
##
## pl.m1.null: Y.re ~ X.re + s(X.re, bs = "cr") + s(X.re, by = c2place.ord,
## bs = "cr") + s(X.re, by = vowel.ord, bs = "cr") + s(X.re,
## rec.date, bs = "fs", xt = "cr", m = 1, k = 5) + s(X.re, speaker,
## bs = "fs", xt = "cr", m = 1, k = 5)
##
## Chi-square test of fREML scores
## -----
## Model Score Edf Chisq Df p.value Sig.
## 1 pl.m1.null -6456.357 14
## 2 pl.m1 -6475.358 16 19.001 2.000 5.596e-09 ***
##
## AIC difference: -20.21, model pl.m1 has lower AIC.plot_smooth(
pl.m1,
view = "X.re",
plot_all= "c2phonation.ord",
cond = list("c2place.ord" = "coronal"),
rug = FALSE
)## Summary:
## * X.re : numeric predictor; with 30 values ranging from 0.001193 to 1.000000.
## * c2phonation.ord : factor; set to the value(s): voiced, voiceless.
## * c2place.ord : factor; set to the value(s): coronal.
## * vowel.ord : factor; set to the value(s): a.
## * rec.date : factor; set to the value(s): 07/02/2017 16:29:14.
## * speaker : factor; set to the value(s): pl02.
plot_diff(
pl.m1,
view = "X.re",
comp = list(c2phonation.ord = c("voiceless", "voiced")),
cond = list("c2place.ord" = "coronal")
)## Summary:
## * X.re : numeric predictor; with 100 values ranging from 0.001193 to 1.000000.
## * c2place.ord : factor; set to the value(s): coronal.
## * vowel.ord : factor; set to the value(s): a.
## * rec.date : factor; set to the value(s): 07/02/2017 16:29:14.
## * speaker : factor; set to the value(s): pl02.
##
## X.re window(s) of significant difference(s):
## 0.001193 - 0.031460
## 0.243328 - 0.283684
## 0.868844 - 1.000000plot_gamsd(
pl.m1,
view = "X.re",
comparison = list(c2phonation.ord = c("voiceless", "voiced")),
conditions = list(c2place.ord = "coronal")
)## Summary:
## * X.re : numeric predictor; with 100 values ranging from 0.001193 to 1.000000.
## * c2phonation.ord : factor; set to the value(s): voiced, voiceless.
## * c2place.ord : factor; set to the value(s): coronal.
## * vowel.ord : factor; set to the value(s): a.
## * rec.date : factor; set to the value(s): 07/02/2017 16:29:14.
## * speaker : factor; set to the value(s): pl02.
plot_gamsd(
pl.m1.ar,
view = "X.re",
comparison = list(c2phonation.ord = c("voiceless", "voiced")),
conditions = list(c2place.ord = "coronal")
)## Summary:
## * X.re : numeric predictor; with 100 values ranging from 0.001193 to 1.000000.
## * c2phonation.ord : factor; set to the value(s): voiced, voiceless.
## * c2place.ord : factor; set to the value(s): coronal.
## * vowel.ord : factor; set to the value(s): a.
## * rec.date : factor; set to the value(s): 07/02/2017 16:29:14.
## * speaker : factor; set to the value(s): pl02.
PL02
pl02_max <- filter(max, speaker == "pl02")
pl02.m1 <- bam(
Y ~
X +
s(X, bs = "cr") +
s(X, by = c2phonation.ord, bs = "cr") +
s(X, by = c2place.ord, bs = "cr") +
s(X, by = vowel.ord, bs = "cr") +
s(X, rec.date, bs = "fs", xt = "cr", m = 1, k = 5),
data = pl02_max,
method = "fREML"
)## Warning in gam.side(sm, X, tol = .Machine$double.eps^0.5): model has
## repeated 1-d smooths of same variable.rho <- start_value_rho(pl02.m1)
pl02.m1.ar <- bam(
Y ~
X +
s(X, bs = "cr") +
s(X, by = c2phonation.ord, bs = "cr") +
s(X, by = c2place.ord, bs = "cr") +
s(X, by = vowel.ord, bs = "cr") +
s(X, rec.date, bs = "fs", xt = "cr", m = 1, k = 5),
data = pl02_max,
method = "fREML",
rho = rho,
AR.start = pl02_max$start.event
)## Warning in gam.side(sm, X, tol = .Machine$double.eps^0.5): model has
## repeated 1-d smooths of same variable.summary(pl02.m1)##
## Family: gaussian
## Link function: identity
##
## Formula:
## Y ~ X + s(X, bs = "cr") + s(X, by = c2phonation.ord, bs = "cr") +
## s(X, by = c2place.ord, bs = "cr") + s(X, by = vowel.ord,
## bs = "cr") + s(X, rec.date, bs = "fs", xt = "cr", m = 1,
## k = 5)
##
## Parametric coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) -2.59019 0.60248 -4.299 1.79e-05 ***
## X 0.29360 0.03819 7.688 2.23e-14 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Approximate significance of smooth terms:
## edf Ref.df F p-value
## s(X) 7.555 7.894 69.913 < 2e-16 ***
## s(X):c2phonation.ordvoiced 8.011 8.702 7.806 1.95e-09 ***
## s(X):c2place.ordvelar 8.883 8.986 316.209 < 2e-16 ***
## s(X):vowel.ordo 8.201 8.788 20.088 < 2e-16 ***
## s(X,rec.date) 189.728 300.000 9.633 < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Rank: 342/343
## R-sq.(adj) = 0.95 Deviance explained = 95.4%
## fREML = 5616 Scale est. = 4.5043 n = 2419pl02.m1.null <- bam(
Y ~
X +
s(X, bs = "cr") +
s(X, by = c2place.ord, bs = "cr") +
s(X, by = vowel.ord, bs = "cr") +
s(X, rec.date, bs = "fs", xt = "cr", m = 1, k = 5),
data = pl02_max,
method = "fREML"
)## Warning in gam.side(sm, X, tol = .Machine$double.eps^0.5): model has
## repeated 1-d smooths of same variable.compareML(pl02.m1, pl02.m1.null)## pl02.m1: Y ~ X + s(X, bs = "cr") + s(X, by = c2phonation.ord, bs = "cr") +
## s(X, by = c2place.ord, bs = "cr") + s(X, by = vowel.ord,
## bs = "cr") + s(X, rec.date, bs = "fs", xt = "cr", m = 1,
## k = 5)
##
## pl02.m1.null: Y ~ X + s(X, bs = "cr") + s(X, by = c2place.ord, bs = "cr") +
## s(X, by = vowel.ord, bs = "cr") + s(X, rec.date, bs = "fs",
## xt = "cr", m = 1, k = 5)
##
## Chi-square test of fREML scores
## -----
## Model Score Edf Chisq Df p.value Sig.
## 1 pl02.m1.null 5638.118 11
## 2 pl02.m1 5615.978 13 22.140 2.000 2.425e-10 ***
##
## AIC difference: -37.43, model pl02.m1 has lower AIC.plot_gamsd(
pl02.m1.ar,
view = "X",
comparison = list(c2phonation.ord = c("voiceless", "voiced")),
conditions = list(c2place.ord = "coronal")
)## Summary:
## * X : numeric predictor; with 100 values ranging from -26.245000 to 59.219800.
## * c2phonation.ord : factor; set to the value(s): voiced, voiceless.
## * c2place.ord : factor; set to the value(s): coronal.
## * vowel.ord : factor; set to the value(s): a.
## * rec.date : factor; set to the value(s): 07/02/2017 16:29:14.
PL03
pl03_max <- filter(max, speaker == "pl03")
pl03.m1 <- bam(
Y ~
X +
s(X, bs = "cr") +
s(X, by = c2phonation.ord, bs = "cr") +
s(X, by = c2place.ord, bs = "cr") +
s(X, by = vowel.ord, bs = "cr") +
s(X, rec.date, bs = "fs", xt = "cr", m = 1, k = 5),
data = pl03_max,
method = "fREML"
)## Warning in gam.side(sm, X, tol = .Machine$double.eps^0.5): model has
## repeated 1-d smooths of same variable.rho <- start_value_rho(pl03.m1)
pl03.m1.ar <- bam(
Y ~
X +
s(X, bs = "cr") +
s(X, by = c2phonation.ord, bs = "cr") +
s(X, by = c2place.ord, bs = "cr") +
s(X, by = vowel.ord, bs = "cr") +
s(X, rec.date, bs = "fs", xt = "cr", m = 1, k = 5),
data = pl03_max,
method = "ML",
rho = rho,
AR.start = pl03_max$start.event
)## Warning in gam.side(sm, X, tol = .Machine$double.eps^0.5): model has
## repeated 1-d smooths of same variable.pl03.m1.ar.null <- bam(
Y ~
X +
s(X, bs = "cr") +
# s(X, by = c2phonation.ord, bs = "cr") +
s(X, by = c2place.ord, bs = "cr") +
s(X, by = vowel.ord, bs = "cr") +
s(X, rec.date, bs = "fs", xt = "cr", m = 1, k = 5),
data = pl03_max,
method = "ML",
rho = rho,
AR.start = pl03_max$start.event
)## Warning in gam.side(sm, X, tol = .Machine$double.eps^0.5): model has
## repeated 1-d smooths of same variable.summary(pl03.m1)##
## Family: gaussian
## Link function: identity
##
## Formula:
## Y ~ X + s(X, bs = "cr") + s(X, by = c2phonation.ord, bs = "cr") +
## s(X, by = c2place.ord, bs = "cr") + s(X, by = vowel.ord,
## bs = "cr") + s(X, rec.date, bs = "fs", xt = "cr", m = 1,
## k = 5)
##
## Parametric coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) -5.15251 0.84915 -6.068 1.63e-09 ***
## X 0.42071 0.05257 8.004 2.35e-15 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Approximate significance of smooth terms:
## edf Ref.df F p-value
## s(X) 7.433 7.793 52.044 < 2e-16 ***
## s(X):c2phonation.ordvoiced 6.740 7.654 4.817 1.54e-05 ***
## s(X):c2place.ordvelar 8.755 8.938 33.136 < 2e-16 ***
## s(X):vowel.ordo 8.770 8.941 20.139 < 2e-16 ***
## s(X,rec.date) 209.072 235.000 26.599 < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Rank: 277/278
## R-sq.(adj) = 0.969 Deviance explained = 97.3%
## fREML = 3995.5 Scale est. = 2.8743 n = 1793pl03.m1.null <- bam(
Y ~
X +
s(X, bs = "cr") +
s(X, by = c2place.ord, bs = "cr") +
s(X, by = vowel.ord, bs = "cr") +
s(X, rec.date, bs = "fs", xt = "cr", m = 1, k = 5),
data = pl03_max,
method = "ML"
)## Warning in gam.side(sm, X, tol = .Machine$double.eps^0.5): model has
## repeated 1-d smooths of same variable.compareML(pl03.m1.ar, pl03.m1.ar.null)## pl03.m1.ar: Y ~ X + s(X, bs = "cr") + s(X, by = c2phonation.ord, bs = "cr") +
## s(X, by = c2place.ord, bs = "cr") + s(X, by = vowel.ord,
## bs = "cr") + s(X, rec.date, bs = "fs", xt = "cr", m = 1,
## k = 5)
##
## pl03.m1.ar.null: Y ~ X + s(X, bs = "cr") + s(X, by = c2place.ord, bs = "cr") +
## s(X, by = vowel.ord, bs = "cr") + s(X, rec.date, bs = "fs",
## xt = "cr", m = 1, k = 5)
##
## Chi-square test of ML scores
## -----
## Model Score Edf Chisq Df p.value Sig.
## 1 pl03.m1.ar.null 3335.866 11
## 2 pl03.m1.ar 3330.848 13 5.018 2.000 0.007 **## Warning in compareML(pl03.m1.ar, pl03.m1.ar.null): AIC is not reliable,
## because an AR1 model is included (rho1 = 0.611727, rho2 = 0.611727).plot_gamsd(
pl03.m1.ar,
view = "X",
comparison = list(c2phonation.ord = c("voiceless", "voiced")),
conditions = list(c2place.ord = "velar")
)## Summary:
## * X : numeric predictor; with 100 values ranging from -34.964200 to 70.078500.
## * c2phonation.ord : factor; set to the value(s): voiced, voiceless.
## * c2place.ord : factor; set to the value(s): velar.
## * vowel.ord : factor; set to the value(s): a.
## * rec.date : factor; set to the value(s): 24/03/2017 14:44:40.
PL04
filter(max, speaker == "pl04") %>%
ggplot(aes(X, Y, colour = c2phonation)) +
geom_point(alpha = 0.5) +
facet_grid(vowel ~ c2place)
filter(max, speaker == "pl04", X > -30) %>%
ggplot(aes(X, Y, colour = c2phonation)) +
geom_point(alpha = 0.5) +
facet_grid(vowel ~ c2place)
pl04_max <- filter(max, speaker == "pl04", X > -30)
pl04.m1 <- bam(
Y ~
X +
s(X, bs = "cr") +
s(X, by = c2phonation.ord, bs = "cr") +
s(X, by = c2place.ord, bs = "cr") +
s(X, by = vowel.ord, bs = "cr") +
s(X, rec.date, bs = "fs", xt = "cr", m = 1, k = 5),
data = pl04_max,
method = "fREML"
)## Warning in gam.side(sm, X, tol = .Machine$double.eps^0.5): model has
## repeated 1-d smooths of same variable.rho <- start_value_rho(pl04.m1)
pl04.m1.ar <- bam(
Y ~
X +
s(X, bs = "cr") +
s(X, by = c2phonation.ord, bs = "cr") +
s(X, by = c2place.ord, bs = "cr") +
s(X, by = vowel.ord, bs = "cr") +
s(X, rec.date, bs = "fs", xt = "cr", m = 1, k = 5),
data = pl04_max,
method = "ML",
rho = rho,
AR.start = pl04_max$start.event
)## Warning in gam.side(sm, X, tol = .Machine$double.eps^0.5): model has
## repeated 1-d smooths of same variable.pl04.m1.ar.null <- bam(
Y ~
X +
s(X, bs = "cr") +
# s(X, by = c2phonation.ord, bs = "cr") +
s(X, by = c2place.ord, bs = "cr") +
s(X, by = vowel.ord, bs = "cr") +
s(X, rec.date, bs = "fs", xt = "cr", m = 1, k = 5),
data = pl04_max,
method = "ML",
rho = rho,
AR.start = pl04_max$start.event
)## Warning in gam.side(sm, X, tol = .Machine$double.eps^0.5): model has
## repeated 1-d smooths of same variable.summary(pl04.m1.ar)##
## Family: gaussian
## Link function: identity
##
## Formula:
## Y ~ X + s(X, bs = "cr") + s(X, by = c2phonation.ord, bs = "cr") +
## s(X, by = c2place.ord, bs = "cr") + s(X, by = vowel.ord,
## bs = "cr") + s(X, rec.date, bs = "fs", xt = "cr", m = 1,
## k = 5)
##
## Parametric coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 3.28296 0.38386 8.553 <2e-16 ***
## X -0.03567 0.03469 -1.028 0.304
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Approximate significance of smooth terms:
## edf Ref.df F p-value
## s(X) 7.538 7.847 31.856 < 2e-16 ***
## s(X):c2phonation.ordvoiced 1.006 1.009 0.296 0.589
## s(X):c2place.ordvelar 8.539 8.876 26.159 < 2e-16 ***
## s(X):vowel.ordo 7.975 8.620 10.694 7.37e-15 ***
## s(X,rec.date) 197.731 230.000 25.617 < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Rank: 272/273
## R-sq.(adj) = 0.975 Deviance explained = 98%
## -ML = 1757.9 Scale est. = 0.72325 n = 1228pl04.m1.null <- bam(
Y ~
X +
s(X, bs = "cr") +
s(X, by = c2place.ord, bs = "cr") +
s(X, by = vowel.ord, bs = "cr") +
s(X, rec.date, bs = "fs", xt = "cr", m = 1, k = 5),
data = pl04_max,
method = "fREML"
)## Warning in gam.side(sm, X, tol = .Machine$double.eps^0.5): model has
## repeated 1-d smooths of same variable.# compareML(pl04.m1, pl04.m1.null)
compareML(pl04.m1.ar, pl04.m1.ar.null)## pl04.m1.ar: Y ~ X + s(X, bs = "cr") + s(X, by = c2phonation.ord, bs = "cr") +
## s(X, by = c2place.ord, bs = "cr") + s(X, by = vowel.ord,
## bs = "cr") + s(X, rec.date, bs = "fs", xt = "cr", m = 1,
## k = 5)
##
## pl04.m1.ar.null: Y ~ X + s(X, bs = "cr") + s(X, by = c2place.ord, bs = "cr") +
## s(X, by = vowel.ord, bs = "cr") + s(X, rec.date, bs = "fs",
## xt = "cr", m = 1, k = 5)
##
## Chi-square test of ML scores
## -----
## Model Score Edf Chisq Df p.value Sig.
## 1 pl04.m1.ar.null 1758.008 11
## 2 pl04.m1.ar 1757.861 13 0.148 2.000 0.863## Warning in compareML(pl04.m1.ar, pl04.m1.ar.null): AIC is not reliable,
## because an AR1 model is included (rho1 = 0.518140, rho2 = 0.518140).## Warning in compareML(pl04.m1.ar, pl04.m1.ar.null): Only small difference in ML...plot_gamsd(
pl04.m1.ar,
view = "X",
comparison = list(c2phonation.ord = c("voiceless", "voiced")),
conditions = list(c2place.ord = "coronal")
)## Summary:
## * X : numeric predictor; with 100 values ranging from -29.959700 to 32.556800.
## * c2phonation.ord : factor; set to the value(s): voiced, voiceless.
## * c2place.ord : factor; set to the value(s): coronal.
## * vowel.ord : factor; set to the value(s): a.
## * rec.date : factor; set to the value(s): 26/05/2017 17:58:11.
acf_plot(resid(pl04.m1.ar), split_by=list(pl04_max$rec.date))
acf_resid(pl04.m1.ar, split_pred = "AR.start")
pl04_a <- filter(max, speaker == "pl04", vowel == "a")
pl04.m1 <- bam(
Y ~
X +
s(X, bs = "cr") +
s(X, by = c2phonation.ord, bs = "cr") +
s(X, by = c2place.ord, bs = "cr") +
s(X, rec.date, bs = "fs", xt = "cr", m = 1, k = 5),
data = pl04_a,
method = "fREML"
)## Warning in gam.side(sm, X, tol = .Machine$double.eps^0.5): model has
## repeated 1-d smooths of same variable.rho <- start_value_rho(pl04.m1)
pl04.m1.ar <- bam(
Y ~
X +
s(X, bs = "cr") +
s(X, by = c2phonation.ord, bs = "cr") +
s(X, by = c2place.ord, bs = "cr") +
s(X, rec.date, bs = "fs", xt = "cr", m = 1, k = 5),
data = pl04_a,
method = "ML",
rho = rho,
AR.start = pl04_a$start.event
)## Warning in gam.side(sm, X, tol = .Machine$double.eps^0.5): model has
## repeated 1-d smooths of same variable.pl04.m1.ar.null <- bam(
Y ~
X +
s(X, bs = "cr") +
# s(X, by = c2phonation.ord, bs = "cr") +
s(X, by = c2place.ord, bs = "cr") +
s(X, rec.date, bs = "fs", xt = "cr", m = 1, k = 5),
data = pl04_a,
method = "ML",
rho = rho,
AR.start = pl04_a$start.event
)## Warning in gam.side(sm, X, tol = .Machine$double.eps^0.5): model has
## repeated 1-d smooths of same variable.summary(pl04.m1.ar)##
## Family: gaussian
## Link function: identity
##
## Formula:
## Y ~ X + s(X, bs = "cr") + s(X, by = c2phonation.ord, bs = "cr") +
## s(X, by = c2place.ord, bs = "cr") + s(X, rec.date, bs = "fs",
## xt = "cr", m = 1, k = 5)
##
## Parametric coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 0.83223 0.46029 1.808 0.0711 .
## X 0.02144 0.04680 0.458 0.6470
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Approximate significance of smooth terms:
## edf Ref.df F p-value
## s(X) 7.479 7.786 24.294 <2e-16 ***
## s(X):c2phonation.ordvoiced 3.384 4.190 0.553 0.575
## s(X):c2place.ordvelar 8.019 8.623 12.720 <2e-16 ***
## s(X,rec.date) 95.926 116.000 29.624 <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Rank: 148/149
## R-sq.(adj) = 0.987 Deviance explained = 98.9%
## -ML = 1101 Scale est. = 0.95795 n = 689compareML(pl04.m1.ar, pl04.m1.ar.null)## pl04.m1.ar: Y ~ X + s(X, bs = "cr") + s(X, by = c2phonation.ord, bs = "cr") +
## s(X, by = c2place.ord, bs = "cr") + s(X, rec.date, bs = "fs",
## xt = "cr", m = 1, k = 5)
##
## pl04.m1.ar.null: Y ~ X + s(X, bs = "cr") + s(X, by = c2place.ord, bs = "cr") +
## s(X, rec.date, bs = "fs", xt = "cr", m = 1, k = 5)
##
## Chi-square test of ML scores
## -----
## Model Score Edf Chisq Df p.value Sig.
## 1 pl04.m1.ar.null 1101.707 9
## 2 pl04.m1.ar 1101.011 11 0.696 2.000 0.499## Warning in compareML(pl04.m1.ar, pl04.m1.ar.null): AIC is not reliable,
## because an AR1 model is included (rho1 = 0.455701, rho2 = 0.455701).## Warning in compareML(pl04.m1.ar, pl04.m1.ar.null): Only small difference in ML...If only /a/ is used, no significance at all. With /o/ and X > -30, no significance, but with all X some significant difference at the very left end of the tongue.
plot_gamsd(
pl04.m1.ar,
view = "X",
comparison = list(c2phonation.ord = c("voiceless", "voiced")),
conditions = list(c2place.ord = "coronal")
)## Summary:
## * X : numeric predictor; with 100 values ranging from -41.892500 to 32.556800.
## * c2phonation.ord : factor; set to the value(s): voiced, voiceless.
## * c2place.ord : factor; set to the value(s): coronal.
## * rec.date : factor; set to the value(s): 26/05/2017 17:59:49.
PL03-PL04
pl34.m1 <- bam(
Y ~
X +
s(X, bs = "cr") +
s(X, by = c2phonation.ord, bs = "cr") +
s(X, by = c2place.ord, bs = "cr") +
s(X, by = vowel.ord, bs = "cr") +
s(X, rec.date, bs = "fs", xt = "cr", m = 1, k = 5) +
s(X, speaker, bs = "fs", xt = "cr", m = 1, k = 5),
data = max_pl_34,
method = "fREML"
)## Warning in gam.side(sm, X, tol = .Machine$double.eps^0.5): model has
## repeated 1-d smooths of same variable.rho <- start_value_rho(pl34.m1)
pl34.m1.ar <- bam(
Y ~
X +
s(X, bs = "cr") +
s(X, by = c2phonation.ord, bs = "cr") +
s(X, by = c2place.ord, bs = "cr") +
s(X, by = vowel.ord, bs = "cr") +
s(X, rec.date, bs = "fs", xt = "cr", m = 1, k = 5) +
s(X, speaker, bs = "fs", xt = "cr", m = 1, k = 5),
data = max_pl_34,
method = "ML",
rho = rho,
AR.start = max_pl_34$start.event
)## Warning in gam.side(sm, X, tol = .Machine$double.eps^0.5): model has
## repeated 1-d smooths of same variable.pl34.m1.ar.null <- bam(
Y ~
X +
s(X, bs = "cr") +
# s(X, by = c2phonation.ord, bs = "cr") +
s(X, by = c2place.ord, bs = "cr") +
s(X, by = vowel.ord, bs = "cr") +
s(X, rec.date, bs = "fs", xt = "cr", m = 1, k = 5) +
s(X, speaker, bs = "fs", xt = "cr", m = 1, k = 5),
data = max_pl_34,
method = "ML",
rho = rho,
AR.start = max_pl_34$start.event
)## Warning in gam.side(sm, X, tol = .Machine$double.eps^0.5): model has
## repeated 1-d smooths of same variable.summary(pl34.m1.ar)##
## Family: gaussian
## Link function: identity
##
## Formula:
## Y ~ X + s(X, bs = "cr") + s(X, by = c2phonation.ord, bs = "cr") +
## s(X, by = c2place.ord, bs = "cr") + s(X, by = vowel.ord,
## bs = "cr") + s(X, rec.date, bs = "fs", xt = "cr", m = 1,
## k = 5) + s(X, speaker, bs = "fs", xt = "cr", m = 1, k = 5)
##
## Parametric coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) -4.8776 3.6453 -1.338 0.181
## X 0.2787 0.2154 1.294 0.196
##
## Approximate significance of smooth terms:
## edf Ref.df F p-value
## s(X) 6.853 7.055 52.880 < 2e-16 ***
## s(X):c2phonation.ordvoiced 5.106 6.157 1.935 0.0706 .
## s(X):c2place.ordvelar 8.572 8.892 38.777 < 2e-16 ***
## s(X):vowel.ordo 7.293 8.174 7.801 1.55e-10 ***
## s(X,rec.date) 354.481 469.000 10.193 < 2e-16 ***
## s(X,speaker) 5.618 8.000 34.261 < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Rank: 522/523
## R-sq.(adj) = 0.959 Deviance explained = 96.4%
## -ML = 5944.5 Scale est. = 2.5902 n = 3130compareML(pl34.m1.ar, pl34.m1.ar.null)## pl34.m1.ar: Y ~ X + s(X, bs = "cr") + s(X, by = c2phonation.ord, bs = "cr") +
## s(X, by = c2place.ord, bs = "cr") + s(X, by = vowel.ord,
## bs = "cr") + s(X, rec.date, bs = "fs", xt = "cr", m = 1,
## k = 5) + s(X, speaker, bs = "fs", xt = "cr", m = 1, k = 5)
##
## pl34.m1.ar.null: Y ~ X + s(X, bs = "cr") + s(X, by = c2place.ord, bs = "cr") +
## s(X, by = vowel.ord, bs = "cr") + s(X, rec.date, bs = "fs",
## xt = "cr", m = 1, k = 5) + s(X, speaker, bs = "fs", xt = "cr",
## m = 1, k = 5)
##
## Chi-square test of ML scores
## -----
## Model Score Edf Chisq Df p.value Sig.
## 1 pl34.m1.ar.null 5947.104 14
## 2 pl34.m1.ar 5944.513 16 2.591 2.000 0.075## Warning in compareML(pl34.m1.ar, pl34.m1.ar.null): AIC is not reliable,
## because an AR1 model is included (rho1 = 0.609938, rho2 = 0.609938).## Warning in compareML(pl34.m1.ar, pl34.m1.ar.null): Only small difference in ML...plot_gamsd(
pl34.m1.ar,
view = "X",
comparison = list(c2phonation.ord = c("voiceless", "voiced")),
conditions = list(c2place.ord = "velar", speaker = "pl04")
)## Summary:
## * X : numeric predictor; with 100 values ranging from -43.836000 to 70.078500.
## * c2phonation.ord : factor; set to the value(s): voiced, voiceless.
## * c2place.ord : factor; set to the value(s): velar.
## * vowel.ord : factor; set to the value(s): a.
## * rec.date : factor; set to the value(s): 24/03/2017 14:44:40.
## * speaker : factor; set to the value(s): pl04.
The models with X, Y are not reliable because the tongue size differs a lot between speakers.
pl34.m1.re <- bam(
Y.re ~
X.re +
s(X.re, bs = "cr") +
s(X.re, by = c2phonation.ord, bs = "cr") +
s(X.re, by = c2place.ord, bs = "cr") +
s(X.re, by = vowel.ord, bs = "cr") +
s(X.re, rec.date, bs = "fs", xt = "cr", m = 1, k = 5) +
s(X.re, speaker, bs = "fs", xt = "cr", m = 1, k = 5),
data = max_pl_34,
method = "fREML"
)## Warning in gam.side(sm, X, tol = .Machine$double.eps^0.5): model has
## repeated 1-d smooths of same variable.rho <- start_value_rho(pl34.m1.re)
pl34.m1.ar.re <- bam(
Y.re ~
X.re +
s(X.re, bs = "cr") +
s(X.re, by = c2phonation.ord, bs = "cr") +
s(X.re, by = c2place.ord, bs = "cr") +
s(X.re, by = vowel.ord, bs = "cr") +
s(X.re, rec.date, bs = "fs", xt = "cr", m = 1, k = 5),
data = max_pl_34,
method = "ML",
rho = rho,
AR.start = max_pl_34$start.event
)## Warning in gam.side(sm, X, tol = .Machine$double.eps^0.5): model has
## repeated 1-d smooths of same variable.pl34.m1.ar.re.null <- bam(
Y.re ~
X.re +
s(X.re, bs = "cr") +
# s(X, by = c2phonation.ord, bs = "cr") +
s(X.re, by = c2place.ord, bs = "cr") +
s(X.re, by = vowel.ord, bs = "cr") +
s(X.re, rec.date, bs = "fs", xt = "cr", m = 1, k = 5),
data = max_pl_34,
method = "ML",
rho = rho,
AR.start = max_pl_34$start.event
)## Warning in gam.side(sm, X, tol = .Machine$double.eps^0.5): model has
## repeated 1-d smooths of same variable.summary(pl34.m1.ar.re)##
## Family: gaussian
## Link function: identity
##
## Formula:
## Y.re ~ X.re + s(X.re, bs = "cr") + s(X.re, by = c2phonation.ord,
## bs = "cr") + s(X.re, by = c2place.ord, bs = "cr") + s(X.re,
## by = vowel.ord, bs = "cr") + s(X.re, rec.date, bs = "fs",
## xt = "cr", m = 1, k = 5)
##
## Parametric coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 0.07931 0.03880 2.044 0.041 *
## X.re 1.10388 0.08357 13.209 <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Approximate significance of smooth terms:
## edf Ref.df F p-value
## s(X.re) 7.433 7.784 38.617 < 2e-16 ***
## s(X.re):c2phonation.ordvoiced 5.673 6.770 2.625 0.0127 *
## s(X.re):c2place.ordvelar 8.417 8.820 14.290 < 2e-16 ***
## s(X.re):vowel.ordo 8.418 8.822 11.068 6.22e-16 ***
## s(X.re,rec.date) 408.292 469.000 12.759 < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Rank: 512/513
## R-sq.(adj) = 0.964 Deviance explained = 96.9%
## -ML = -6142.8 Scale est. = 0.0010642 n = 3130compareML(pl34.m1.ar.re, pl34.m1.ar.re.null)## pl34.m1.ar.re: Y.re ~ X.re + s(X.re, bs = "cr") + s(X.re, by = c2phonation.ord,
## bs = "cr") + s(X.re, by = c2place.ord, bs = "cr") + s(X.re,
## by = vowel.ord, bs = "cr") + s(X.re, rec.date, bs = "fs",
## xt = "cr", m = 1, k = 5)
##
## pl34.m1.ar.re.null: Y.re ~ X.re + s(X.re, bs = "cr") + s(X.re, by = c2place.ord,
## bs = "cr") + s(X.re, by = vowel.ord, bs = "cr") + s(X.re,
## rec.date, bs = "fs", xt = "cr", m = 1, k = 5)
##
## Chi-square test of ML scores
## -----
## Model Score Edf Chisq Df p.value Sig.
## 1 pl34.m1.ar.re.null -6138.175 11
## 2 pl34.m1.ar.re -6142.819 13 4.643 2.000 0.010 **## Warning in compareML(pl34.m1.ar.re, pl34.m1.ar.re.null): AIC is not
## reliable, because an AR1 model is included (rho1 = 0.590508, rho2 =
## 0.590508).## Warning in compareML(pl34.m1.ar.re, pl34.m1.ar.re.null): Only small difference in ML...plot_gamsd(
pl34.m1.ar.re,
view = "X.re",
comparison = list(c2phonation.ord = c("voiceless", "voiced")),
conditions = list(c2place.ord = "coronal")
)## Summary:
## * X.re : numeric predictor; with 100 values ranging from 0.015449 to 0.982036.
## * c2phonation.ord : factor; set to the value(s): voiced, voiceless.
## * c2place.ord : factor; set to the value(s): coronal.
## * vowel.ord : factor; set to the value(s): a.
## * rec.date : factor; set to the value(s): 24/03/2017 14:44:40.
plot_gamsd(
pl34.m1.ar.re,
view = "X.re",
comparison = list(c2phonation.ord = c("voiceless", "voiced")),
conditions = list(c2place.ord = "velar")
)## Summary:
## * X.re : numeric predictor; with 100 values ranging from 0.015449 to 0.982036.
## * c2phonation.ord : factor; set to the value(s): voiced, voiceless.
## * c2place.ord : factor; set to the value(s): velar.
## * vowel.ord : factor; set to the value(s): a.
## * rec.date : factor; set to the value(s): 24/03/2017 14:44:40.
Italian
it.m1 <- bam(
Y.re ~
X.re +
s(X.re, bs = "cr") +
s(X.re, by = c2phonation.ord, bs = "cr") +
s(X.re, by = c2place.ord, bs = "cr") +
s(X.re, by = vowel.ord, bs = "cr") +
s(X.re, rec.date, bs = "fs", xt = "cr", m = 1, k = 5) +
s(X.re, speaker, bs = "fs", xt = "cr", m = 1, k = 5),
data = max_it_12,
method = "fREML"
)## Warning in gam.side(sm, X, tol = .Machine$double.eps^0.5): model has
## repeated 1-d smooths of same variable.rho <- start_value_rho(it.m1)
it.m1.ar <- bam(
Y.re ~
X.re +
s(X.re, bs = "cr") +
s(X.re, by = c2phonation.ord, bs = "cr") +
s(X.re, by = c2place.ord, bs = "cr") +
s(X.re, by = vowel.ord, bs = "cr") +
s(X.re, rec.date, bs = "fs", xt = "cr", m = 1, k = 5) +
s(X.re, speaker, bs = "fs", xt = "cr", m = 1, k = 5),
data = max_it_12,
method = "ML",
rho = rho,
AR.start = max_it_12$start.event
)## Warning in gam.side(sm, X, tol = .Machine$double.eps^0.5): model has
## repeated 1-d smooths of same variable.summary(it.m1.ar)##
## Family: gaussian
## Link function: identity
##
## Formula:
## Y.re ~ X.re + s(X.re, bs = "cr") + s(X.re, by = c2phonation.ord,
## bs = "cr") + s(X.re, by = c2place.ord, bs = "cr") + s(X.re,
## by = vowel.ord, bs = "cr") + s(X.re, rec.date, bs = "fs",
## xt = "cr", m = 1, k = 5) + s(X.re, speaker, bs = "fs", xt = "cr",
## m = 1, k = 5)
##
## Parametric coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 0.25090 0.06259 4.008 6.26e-05 ***
## X.re 0.80000 0.21532 3.715 0.000207 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Approximate significance of smooth terms:
## edf Ref.df F p-value
## s(X.re) 5.516 6.082 3.409 0.00394 **
## s(X.re):c2phonation.ordvoiced 5.106 6.209 5.491 1.33e-05 ***
## s(X.re):c2place.ordvelar 8.706 8.942 101.743 < 2e-16 ***
## s(X.re):vowel.ordo 5.286 6.405 8.554 1.45e-09 ***
## s(X.re,rec.date) 177.731 415.000 1.097 < 2e-16 ***
## s(X.re,speaker) 6.607 8.000 74.894 < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Rank: 467/468
## R-sq.(adj) = 0.941 Deviance explained = 94.5%
## -ML = -6713.9 Scale est. = 0.0017165 n = 3165it.m1.ar.null <- bam(
Y.re ~
X.re +
s(X.re, bs = "cr") +
# s(X.re, by = c2phonation.ord, bs = "cr") +
s(X.re, by = c2place.ord, bs = "cr") +
s(X.re, by = vowel.ord, bs = "cr") +
s(X.re, rec.date, bs = "fs", xt = "cr", m = 1, k = 5) +
s(X.re, speaker, bs = "fs", xt = "cr", m = 1, k = 5),
data = max_it_12,
method = "ML",
rho = rho,
AR.start = max_it_12$start.event
)## Warning in gam.side(sm, X, tol = .Machine$double.eps^0.5): model has
## repeated 1-d smooths of same variable.it.m1.null <- bam(
Y.re ~
X.re +
s(X.re, bs = "cr") +
s(X.re, by = c2place.ord, bs = "cr") +
s(X.re, by = vowel.ord, bs = "cr") +
s(X.re, rec.date, bs = "fs", xt = "cr", m = 1, k = 5) +
s(X.re, speaker, bs = "fs", xt = "cr", m = 1, k = 5),
data = max_it_12,
method = "ML"
)## Warning in gam.side(sm, X, tol = .Machine$double.eps^0.5): model has
## repeated 1-d smooths of same variable.compareML(it.m1.ar, it.m1.ar.null)## it.m1.ar: Y.re ~ X.re + s(X.re, bs = "cr") + s(X.re, by = c2phonation.ord,
## bs = "cr") + s(X.re, by = c2place.ord, bs = "cr") + s(X.re,
## by = vowel.ord, bs = "cr") + s(X.re, rec.date, bs = "fs",
## xt = "cr", m = 1, k = 5) + s(X.re, speaker, bs = "fs", xt = "cr",
## m = 1, k = 5)
##
## it.m1.ar.null: Y.re ~ X.re + s(X.re, bs = "cr") + s(X.re, by = c2place.ord,
## bs = "cr") + s(X.re, by = vowel.ord, bs = "cr") + s(X.re,
## rec.date, bs = "fs", xt = "cr", m = 1, k = 5) + s(X.re, speaker,
## bs = "fs", xt = "cr", m = 1, k = 5)
##
## Chi-square test of ML scores
## -----
## Model Score Edf Chisq Df p.value Sig.
## 1 it.m1.ar.null -6702.103 14
## 2 it.m1.ar -6713.863 16 11.761 2.000 7.805e-06 ***## Warning in compareML(it.m1.ar, it.m1.ar.null): AIC is not reliable, because
## an AR1 model is included (rho1 = 0.762798, rho2 = 0.762798).plot_gamsd(
it.m1.ar,
view = "X.re",
comparison = list(c2phonation.ord = c("voiceless", "voiced")),
conditions = list(c2place.ord = "coronal")
)## Summary:
## * X.re : numeric predictor; with 100 values ranging from 0.000000 to 0.995850.
## * c2phonation.ord : factor; set to the value(s): voiced, voiceless.
## * c2place.ord : factor; set to the value(s): coronal.
## * vowel.ord : factor; set to the value(s): a.
## * rec.date : factor; set to the value(s): 29/11/2016 15:10:52.
## * speaker : factor; set to the value(s): it01.
IT01
it01_max <- filter(max, speaker == "it01")
it01.m1 <- bam(
Y ~
X.re +
s(X, bs = "cr") +
s(X, by = c2phonation.ord, bs = "cr") +
s(X, by = c2place.ord, bs = "cr") +
s(X, by = vowel.ord, bs = "cr") +
s(X, rec.date, bs = "fs", xt = "cr", m = 1, k = 5),
data = it01_max,
method = "fREML"
)## Warning in gam.side(sm, X, tol = .Machine$double.eps^0.5): model has
## repeated 1-d smooths of same variable.rho <- start_value_rho(it01.m1)
it01.m1.ar <- bam(
Y ~
X +
s(X, bs = "cr") +
s(X, by = c2phonation.ord, bs = "cr") +
s(X, by = c2place.ord, bs = "cr") +
s(X, by = vowel.ord, bs = "cr") +
s(X, rec.date, bs = "fs", xt = "cr", m = 1, k = 5),
data = it01_max,
method = "ML",
rho = rho,
AR.start = it01_max$start.event
)## Warning in gam.side(sm, X, tol = .Machine$double.eps^0.5): model has
## repeated 1-d smooths of same variable.summary(it01.m1.ar)##
## Family: gaussian
## Link function: identity
##
## Formula:
## Y ~ X + s(X, bs = "cr") + s(X, by = c2phonation.ord, bs = "cr") +
## s(X, by = c2place.ord, bs = "cr") + s(X, by = vowel.ord,
## bs = "cr") + s(X, rec.date, bs = "fs", xt = "cr", m = 1,
## k = 5)
##
## Parametric coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) -4.73141 0.30682 -15.42 <2e-16 ***
## X 0.76532 0.02666 28.70 <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Approximate significance of smooth terms:
## edf Ref.df F p-value
## s(X) 7.764 7.944 181.554 < 2e-16 ***
## s(X):c2phonation.ordvoiced 5.037 6.136 9.480 2.06e-10 ***
## s(X):c2place.ordvelar 8.822 8.979 183.531 < 2e-16 ***
## s(X):vowel.ordo 6.862 7.808 11.566 1.19e-15 ***
## s(X,rec.date) 92.680 225.000 1.976 < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Rank: 267/268
## R-sq.(adj) = 0.979 Deviance explained = 98%
## -ML = 3488.2 Scale est. = 4.0701 n = 1932it01.m1.ar.null <- bam(
Y ~
X +
s(X, bs = "cr") +
# s(X, by = c2phonation.ord, bs = "cr") +
s(X, by = c2place.ord, bs = "cr") +
s(X, by = vowel.ord, bs = "cr") +
s(X, rec.date, bs = "fs", xt = "cr", m = 1, k = 5),
data = it01_max,
method = "ML",
rho = rho,
AR.start = it01_max$start.event
)## Warning in gam.side(sm, X, tol = .Machine$double.eps^0.5): model has
## repeated 1-d smooths of same variable.compareML(it01.m1.ar, it01.m1.ar.null)## it01.m1.ar: Y ~ X + s(X, bs = "cr") + s(X, by = c2phonation.ord, bs = "cr") +
## s(X, by = c2place.ord, bs = "cr") + s(X, by = vowel.ord,
## bs = "cr") + s(X, rec.date, bs = "fs", xt = "cr", m = 1,
## k = 5)
##
## it01.m1.ar.null: Y ~ X + s(X, bs = "cr") + s(X, by = c2place.ord, bs = "cr") +
## s(X, by = vowel.ord, bs = "cr") + s(X, rec.date, bs = "fs",
## xt = "cr", m = 1, k = 5)
##
## Chi-square test of ML scores
## -----
## Model Score Edf Chisq Df p.value Sig.
## 1 it01.m1.ar.null 3509.547 11
## 2 it01.m1.ar 3488.231 13 21.316 2.000 5.527e-10 ***## Warning in compareML(it01.m1.ar, it01.m1.ar.null): AIC is not reliable,
## because an AR1 model is included (rho1 = 0.745137, rho2 = 0.745137).plot_gamsd(
it01.m1.ar,
view = "X",
comparison = list(c2phonation.ord = c("voiceless", "voiced")),
conditions = list(c2place.ord = "coronal")
)## Summary:
## * X : numeric predictor; with 100 values ranging from -40.731200 to 54.425500.
## * c2phonation.ord : factor; set to the value(s): voiced, voiceless.
## * c2place.ord : factor; set to the value(s): coronal.
## * vowel.ord : factor; set to the value(s): a.
## * rec.date : factor; set to the value(s): 29/11/2016 15:10:52.
IT02
it02_max <- filter(max, speaker == "it02")
it02.m1 <- bam(
Y ~
X.re +
s(X, bs = "cr") +
s(X, by = c2phonation.ord, bs = "cr") +
s(X, by = c2place.ord, bs = "cr") +
s(X, by = vowel.ord, bs = "cr") +
s(X, rec.date, bs = "fs", xt = "cr", m = 1, k = 5),
data = it02_max,
method = "fREML"
)## Warning in gam.side(sm, X, tol = .Machine$double.eps^0.5): model has
## repeated 1-d smooths of same variable.rho <- start_value_rho(it02.m1)
it02.m1.ar <- bam(
Y ~
X +
s(X, bs = "cr") +
s(X, by = c2phonation.ord, bs = "cr") +
s(X, by = c2place.ord, bs = "cr") +
s(X, by = vowel.ord, bs = "cr") +
s(X, rec.date, bs = "fs", xt = "cr", m = 1, k = 5),
data = it02_max,
method = "ML",
rho = rho,
AR.start = it02_max$start.event
)## Warning in gam.side(sm, X, tol = .Machine$double.eps^0.5): model has
## repeated 1-d smooths of same variable.summary(it02.m1.ar)##
## Family: gaussian
## Link function: identity
##
## Formula:
## Y ~ X + s(X, bs = "cr") + s(X, by = c2phonation.ord, bs = "cr") +
## s(X, by = c2place.ord, bs = "cr") + s(X, by = vowel.ord,
## bs = "cr") + s(X, rec.date, bs = "fs", xt = "cr", m = 1,
## k = 5)
##
## Parametric coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) -1.67360 0.52437 -3.192 0.00145 **
## X 0.65159 0.03157 20.640 < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Approximate significance of smooth terms:
## edf Ref.df F p-value
## s(X) 6.386 7.189 57.403 < 2e-16 ***
## s(X):c2phonation.ordvoiced 6.589 7.613 4.927 9.93e-06 ***
## s(X):c2place.ordvelar 8.630 8.910 52.382 < 2e-16 ***
## s(X):vowel.ordo 5.937 7.020 9.062 6.16e-11 ***
## s(X,rec.date) 72.997 185.000 1.401 < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Rank: 227/228
## R-sq.(adj) = 0.916 Deviance explained = 92.2%
## -ML = 2803.6 Scale est. = 9.778 n = 1233it02.m1.ar.null <- bam(
Y ~
X +
s(X, bs = "cr") +
# s(X, by = c2phonation.ord, bs = "cr") +
s(X, by = c2place.ord, bs = "cr") +
s(X, by = vowel.ord, bs = "cr") +
s(X, rec.date, bs = "fs", xt = "cr", m = 1, k = 5),
data = it02_max,
method = "ML",
rho = rho,
AR.start = it02_max$start.event
)## Warning in gam.side(sm, X, tol = .Machine$double.eps^0.5): model has
## repeated 1-d smooths of same variable.compareML(it02.m1.ar, it02.m1.ar.null)## it02.m1.ar: Y ~ X + s(X, bs = "cr") + s(X, by = c2phonation.ord, bs = "cr") +
## s(X, by = c2place.ord, bs = "cr") + s(X, by = vowel.ord,
## bs = "cr") + s(X, rec.date, bs = "fs", xt = "cr", m = 1,
## k = 5)
##
## it02.m1.ar.null: Y ~ X + s(X, bs = "cr") + s(X, by = c2place.ord, bs = "cr") +
## s(X, by = vowel.ord, bs = "cr") + s(X, rec.date, bs = "fs",
## xt = "cr", m = 1, k = 5)
##
## Chi-square test of ML scores
## -----
## Model Score Edf Chisq Df p.value Sig.
## 1 it02.m1.ar.null 2813.488 11
## 2 it02.m1.ar 2803.592 13 9.897 2.000 5.034e-05 ***## Warning in compareML(it02.m1.ar, it02.m1.ar.null): AIC is not reliable,
## because an AR1 model is included (rho1 = 0.735050, rho2 = 0.735050).plot_gamsd(
it02.m1.ar,
view = "X",
comparison = list(c2phonation.ord = c("voiceless", "voiced")),
conditions = list(c2place.ord = "coronal")
)## Summary:
## * X : numeric predictor; with 100 values ranging from -44.949000 to 62.666500.
## * c2phonation.ord : factor; set to the value(s): voiced, voiceless.
## * c2place.ord : factor; set to the value(s): coronal.
## * vowel.ord : factor; set to the value(s): a.
## * rec.date : factor; set to the value(s): 12/12/2016 14:45:14.